NIPT: Overview of Technology
Morry Fiddler, PhD
Insight Medical Genetics
Professor Emeritus, DePaul University
Haichuan Zhang, PhD
Celula (China) Medical Technology, Ltd.
Since its introduction and support by the American College of Obstetricians and Gynecologists in 2011, noninvasive prenatal testing (NIPT) has undergone rapid adoption and evolution.1 NIPT rests on a history of prenatal diagnostics to detect chromosomal disorders that began in the 1960s.2 Since that time, the addition of chorionic villus sampling (CVS) to the list of invasive procedure options fueled the desire to obtain prenatal assessments at earlier stages of pregnancy. This advance was followed by the development of noninvasive approaches to avoid the procedural risks and, for many women, the discomforts of both amniocentesis and CVS. The desire for improved sensitivities and specificities of screening converged with a nascent body of work regarding the presence and nature of circulating cell-free DNA (cfDNA),3-5 the development of massively parallel sequencing (MPS),6,7 and techniques to count DNA fragments. This convergence and continued advancement of technologies, coupled with a deepening understanding of cfDNA, has given women’s health care providers a powerful and expanding screening tool to assess the genomic status of a developing fetus. With new technology advancements, NIPT using cfDNA and fetal cells will further evolve to replace amniocentesis and CVS in the future.
Biologic Basis of NIPT
The presence of cfDNA has been known for about 70 years.8 Approximately 10% of the DNA in maternal circulation is of fetal origin, although that proportion ranges from <3% to >20% in any individual9; the remaining ~90% of circulating DNA is maternal. Most of this cfDNA is derived from the placenta,5 with a considerably lesser contribution from the fetus itself. The DNA in circulation is typically found as small fragments of 150 to 200 base pairs,10 which is thought to be derived mostly from DNA generated by apoptosis (programmed cell death) of placental cells, but may also be from live cells in a much smaller quantity.
In addition to the size of the DNA fragments in circulation, 2 features of cfDNA are of particular importance to the design and implementation of technologies for the noninvasive assessment of fetal status: the proportion of fetal DNA relative to the maternal contribution in circulation during pregnancy, known as the fetal fraction, and the timing of a detectable level of fetal DNA in circulation, which is usually by 7 weeks.11,12 Additionally, fetal DNA is continually being refreshed with a half-life of <20 minutes and disappears from maternal circulation within a few hours postpartum, which eliminates concerns of a “carryover” effect from one pregnancy to the next.12
The presence of fetal cells in maternal circulation is much rarer compared to cfDNA. The number of fetal cells that can be successfully identified and isolated from 10 mL of maternal blood is often reported as well below 100. The presence of fetal cells in maternal circulation has been reported as nucleated red blood cells, trophoblasts, lymphocytes, and granulocytes.13 The process of fetal cell isolation is generally much more tedious than cfDNA, and the efficiency of isolation can be inconsistent from sample to sample.
Despite these challenges, fetal cells, once isolated, likely contain the complete genetic information of the fetus without maternal background and limitations from the short DNA fragmentation in cfDNA. Fetal cells in maternal circulation provide a path for an accurate noninvasive analysis of all genetic diseases beyond aneuploidy.
To receive CME credit, please read the articles and go to www.omniaeducation.com/NIPT to access the post-test and evaluation.
This supplement is designed to provide ObGyn clinicians with current information on the cell-free DNA screening test options available for fetal chromosomal abnormalities. These screening tests are commonly referred to as Noninvasive Prenatal Screening (NIPS). In August 2020, the American College of Obstetricians and Gynecologists (ACOG) issued a Practice Bulletin entitled “Screening for Fetal Chromosomal Abnormalities” (PB #226). This Practice Bulletin included expanded information regarding the use of NIPS in all patients regardless of maternal age or baseline risk. It also identified NIPS as the most sensitive and specific test for screening for the most common aneuploidies. The authors of this supplement provide additional information on the technology, performance, and clinical utilization of NIPS testing.
Ann Early has nothing to disclose.
Genevieve L. Fairbrother MD, MPH, FACOG has nothing to disclose.
Morry Fiddler, PhD receives a salary from Insight Medical Genetics.
Barry A. Fiedel, PhD has nothing to disclose.
Amanda Hilferty has nothing to disclose.
Robert Schneider, MSW has nothing to disclose.
Lee P. Shulman, MD, FACMG, FACOG receives consulting fees from Biogix, Celula, Cooper Surgical, Natera, and Vermillion/Aspira and is a speaker for Bayer, Lupin Pharmaceuticals, Inc., and Myriad.
Andrew F. Wagner, MD, FACMG, FACOG has nothing to disclose.
Haichuan Zhang, PhD has ownership interest in Celula China Medical Technology Co.
After participating in this educational activity, participants should be better able to:
- Overcome barriers and demonstrate competency in integrating ACOG/Society for Maternal-Fetal Medicine Noninvasive Prenatal Testing Committee Opinions/Practice Bulletins recommendations into clinical decisionmaking surrounding prenatal visits for all pregnant patients.
- Explain the benefits and disadvantages of traditional fetal chromosomal aneuploidy screening tests compared with noninvasive screening tests.
- Define the technology that is the basis of the various noninvasive screening tests, including the role that fetal fraction plays in influencing results.
- Explain the expanding role of NIPS in the general obstetrical population.
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Global Learning Collaborative designates this enduring material for a maximum of 1 AMA PRA Category 1 Credits™. Physicians should claim only the credit commensurate with the extent of their participation in the activity.
This activity is designed to meet the educational needs of the obstetrician and gynecologist, family physician, internal medicine physician, physician assistant, nurse practitioner, and certified nurse midwife.
This activity is supported by an independent educational grant from Roche Diagnostics.
The views and opinions expressed in this educational activity are those of the faculty and do not necessarily represent the views of GLC and Omnia Education. This presentation is not intended to define an exclusive course of patient management; the participant should use his/her clinical judgment, knowledge, experience, and diagnostic skills in applying or adopting for professional use any of the information provided herein. Any procedures, medications, or other courses of diagnosis or treatment discussed or suggested in this activity should not be used by clinicians without evaluation of their patients’ conditions and possible contraindications or dangers in use, review of any applicable manufacturer’s product information, and comparison with recommendations of other authorities. Links to other sites may be provided as additional sources of information. Once you elect to link to a site outside of Omnia Education you are subject to the terms and conditions of use, including copyright and licensing restriction, of that site.
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- American College of Obstetricians and Gynecologists Committee on Genetics. Committee Opinion No. 545: noninvasive prenatal testing for fetal aneuploidy. Obstet Gynecol. 2012;120(6):1532-1534.
- Jacobsen CB, Barth RH. Intrauterine diagnosis and management of genetic defects. Am J Obstet Gynecol. 1967;99(6):796-807.
- Lo YM, Corbetta N, Chamberlain PF, et al. Presence of fetal DNA in maternal plasma and serum. Lancet. 1997;350(9076):485-487.
- Lo YM, Tein MS, Lan TK, et al. Quantitative analysis of fetal DNA in maternal plasma and serum: implications for noninvasive prenatal diagnosis. Am J Hum Genet. 1998;62(4):768-775.
- Alberry M, Maddocks D, Jones M, et al. Free fetal DNA in maternal plasma in anembryonic pregnancies: confirmation that the origin is the trophoblast. Prenat Diagn. 2007;27(5):415-418.
- Tucker T, Marra M, Friedman JM. Massively parallel sequencing: the next big thing in genetic medicine. Am J Hum Genet. 2009;85(2):142-154.
- Levy S, Sutton G, Ng PC, et al. The diploid genome sequence of an individual human. PLoS Biol. 2007;5(10):e254.
- Mandel P, Metais P. Les aides nucléiques du plasma sanguine che l’homme [Nuclear acids in human blood plasma]. C R Seances Soc Biol Fil. 1948;142(3-4):241-243.
- Taglauer ES, Wilkins-Haug L, Bianchi DW. Review: cell-free DNA in the maternal circulation as an indication of placental health and disease. Placenta. 2014;35(suppl):S64-S68.
- Chan KC, Zhang J, Hui AB, et al. Size distribution of maternal and fetal DNA in maternal plasma. Clin Chem. 2004;50(1):88-92.
- Kinnings SL, Geis JA, Almasri E, et al. Factors affecting levels of circulating cell-free fetal DNA in maternal plasma and their implications for noninvasive prenatal testing. Prenat Diagn. 2015;35(8):816-822.
- Bischoff FZ, Lewis DE, Simpson JL. Cell-free fetal DNA in maternal blood: kinetics, source and structure. Hum Reprod Update. 2005;11(1):59-67.
- Simpson LJ, Elias S. Isolating fetal cells in maternal circulation for prenatal diagnosis. Prenat Diagn. 1994;14(13):1229-1242.
- Sparks AB, Wang ET, Struble CA, et al. Selective analysis of cell-free DNA in maternal blood for evaluation in maternal blood for evaluation of fetal trisomy. Prenat Diagn. 2012;32(1):3-9.
- Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci U S A. 2008;105(42):16266-16271.
- Moorthie S, Mattocks CJ, Wright CF. Review of massively parallel DNA sequencing technologies. Hugo J. 2011;5(1-4):1-12.
- Benjamini Y, Speed TP. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res. 2012;40(10):e72.
- Stokowski R, Wang E, White K, et al. Clinical performance of noninvasive prenatal testing using targeted cell-free DNA analysis in maternal plasma with microarrays or next generation sequencing is consistent across multiple controlled clinical studies. Prenat Diagn. 2015;35(12):1243-1246.
- Zimmerman B, Hill M, Gemelos G, et al. Noninvasive prenatal aneuploidy testing of chromosomes 13, 18, 21, X, and Y using targeted sequencing polymorphic loci. Prenat Diagn. 2012;32(13):1233-1241.
- Nicolaides KH, Syngelaki A, Gil M, Atanasova V, Markova D. Validation of targeted sequencing of single-nucleotide polymorphisms for non invasive prenatal detection of aneuploidy of chromosomes 13, 18, 21, X, and Y. Prenat Diagn. 2013;33(6):575-579.
- Norton ME, Jacobsson B, Swamy GK, et al. Cell-free DNA analysis for noninvasive examination of trisomy. N Engl J Med. 2015;372(17):1589-1597.
- Juneau K, Bogad PE, Huang S, et al. Microarray-based cell-free DNA analysis improves noninvasive prenatal testing. Fetal Diagn Ther. 2014;36(4):282-286.
- Ryan A, Hunkapillar N, Banjevic M, et al. Validation of an enhanced version of a single-nucleotide polymorphism-based noninvasive prenatal test for detection of fetal aneuploidies. Fetal Diagn Ther. 2016;40(3):219-223.
- Ali MM, Li F, Zhang Z, et al. Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine. Chem Soc Rev. 2014;43(10):3324-3341.
- Dahl F, Ericsson O, Karlberg O, et al. Imaging single DNA molecules for high precision NIPT. Sci Rep. 2018;8(1):4549.
- Ericsson O, Ahola T, Dahl F, et al. Clinical validation of a novel automated cell-free DNA screening assay for trisomies 21, 13, and 18 in maternal plasma. Prenat Diagn. 2019;39(11):1011-1015.
- Bianchi DW, Platt LD, Goldberg JD, et al. Genome-wide fetal aneuploidy detection by maternal plasma DNA sequencing. Obstet Gynecol. 2012;119(5):890-901.
- Sehnert AJ, Rhees B, Comstock D, et al. Optimal detection of fetal chromosomal abnormalities by massively parallel DNA sequencing of cell-free DNA from maternal blood. Clin Chem. 2011;57(7):1042-1049.
- Palomaki GE, Deciu C, Kloza EM, et al. DNA sequencing of maternal plasma reliably identifies trisomy 18 and trisomy 13 as well as Down syndrome: an international collaborative study. Genet Med. 2012;14(3):296-305.
- Canick JA, Palomaki GE, Kloza EM, Lambert-Messerlian GM, Haddow JE. The impact of maternal plasma DNA fetal fraction on next generation sequencing tests for common fetal aneuploidies. Prenat Diagn. 2013;33(7):667-674.
- 31. Crosetto B, Cantwell M. Noninvasive prenatal testing (NIPT): the next best aneuploidy screen? MultiCare Women & Children’s Grand Rounds Continuing Medical Education. p. 27. https://www.multicare.org/file_viewer.php?id=8440&title=wcgr1212. Published 2012. Accessed February 9, 2019.
- Gregg AR, Skotko BG, Benkendorf JL, et al. Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics. Genet Med. 2016;18(10):1056-1065.
- Wang E, Batey A, Struble C, Musci T, Song K, Oliphant A. Gestational age and maternal weight effects on fetal cell-free DNA in maternal plasma. Prenat Diagn. 2013;33(7):662-666.